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	<title>P3DB: Plant Protein Phosphorylation Database</title>
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<?php
$item = $_GET['item'];
if (!empty($item)) {
        if (strcmp($item,"probability")==0) { ?>
                <h3><u>Probability</u></h3>
                <u>Definition:</u> The probability score is based on the probability that the peptide
                is a random match to the spectral data.
<?php   } elseif (strcmp($item,"mascotscore")==0) { ?>
                <h3><u>Mascot score</u></h3>
                <u>Definition:</u> Score from search engine Mascot based on Ions score which is -10*Log(P),
                where P is the probability that the observed match is a random event.
<?php   } elseif (strcmp($item,"spectrumcount")==0) { ?>
                <h3><u>Spectrum count</u></h3>
                <u>Definition:</u> For peptide--the total number of MS/MS spectra associated with any given peptide.
                For protein--sum of MS/MS spectrum counts for all identified peptides in any given protein.
<?php   } elseif (strcmp($item,"xcorr")==0) { ?>
                <h3><u>XCorr</u></h3>
                <u>Definition:</u> Cross-correlation value between the observed peptide fragment mass spectrum and
                the one theoretically predicted.
                <br/>
                <u>Interpretation:</u> Cross-correlation value is used to measure "whether the match is good".
                <table border="1">
                        <tr><td>XCorr</td><td>Is the match good?</td></tr>
                        <tr><td>>4.5</td><td>No doubt</td></tr>
                        <tr><td>>3.5</td><td>Excellent</td></tr>
                        <tr><td>>2.5</td><td>Good</td></tr>
                        <tr><td>>1.5</td><td>Maybe</td></tr>
                </table>
<?php   } elseif (strcmp($item,"deltacn")==0) { ?>
                <h3><u>&Delta;Cn</u></h3>
                <u>Definition:</u> The cross-correlation difference between the first and the second peptide hit.
                <br/>
                <u>Interpretation:</u> &Delta;Cn is used to measure "whether one spectra match better than another"
                <table border="1">
                        <tr><td>&Delta;Cn</td><td>Does one spectra match better than another</td></tr>
                        <tr><td>>0.3</td><td>Great</td></tr>
                        <tr><td>>0.1</td><td>Good</td></tr>
                </table>
<?php   } elseif (strcmp($item,"sf")==0) { ?>
                <h3><u>Sf</u></h3>
                <u>Definition:</u> The final score, Sf, indicates how good the protein and peptide match is between the
                experimental MS/MS data and the theoretical data.
<?php   } elseif (strcmp($item,"charge")==0) { ?>
                <h3><u>Charge</u></h3>
                <u>Definition:</u> The charge state of the peptide.
<?php   } elseif (strcmp($item,"mh")==0) { ?>
                <h3><u>MH+</u></h3>
                <u>Definition:</u> Peptide mass.
<?php   } elseif (strcmp($item,"masserr")==0) { ?>
                <h3><u>Mass error</u></h3>
                <u>Definition:</u> The different between observed peptide mass and theoretical peptide mass.
<?php   } elseif (strcmp($item,"accession")==0) { ?>
                Currently, supported protein accession numbers in P<sup>3</sup>DB are UniProt <u>accession number/identifier</u>,
                <u>RefSeq accession number</u>, <u>NCBI gi number</u> and <u>TAIR agi code</u>.
<?php   } elseif (strcmp($item,"score")==0) { ?>
                <h3><u>Score</u></h3>
                <u>Definition:</u> Protein consensus score. It is calculated as “Sum of Primaries * 10,
                Secondaries * 8, Tertiaries * 6, Quaternaries * 4, etc.”<br/>
                <u>Interpretation:</u> When performing an MS/MS search, protein scores are basis for ranking protein hits.
<?php   } elseif (strcmp($item,"pepsrc")==0) { ?>
                Peptide source organism is the organism from which the phospho-peptides come.
                If the peptide source organism's genome information is not completely available, e.g. oilseed rape,
                we will use selected plant protein database for searching for matching proteins.
                In that case, the organisms of matching proteins may be different from the source organism.
                see <a href="../releasenotes.php">release notes</a>.
<?php   } elseif (strcmp($item,"pfam")==0) { ?>
                Protein Pfam domains are predicted by <a href="http://pfam.sanger.ac.uk/">Sanger Pfam online service</a>
                (Pfam 22.0) with e-value cutoff 10<sup>-10</sup>.
<?php   } elseif (strcmp($item,"goslim")==0) { ?>
                GO annotations are based on <a href="http://www.ebi.ac.uk/GO/">Gene Ontology @ EBI</a>. Currently, the oilseed rape
                phosphorylation dataset has been annotated with GO categories.
<?php   } elseif (strcmp($item,"modify")==0) { ?>
                An amino acid M (methionine) in brown color in a phosphopeptide indicates an oxidation on this residue.<br>
                An amino acid C (cysteine) in brown color in a phosphopeptide indicates a carboxyamidomethylation on this residue.<br>
<?php   } elseif (strcmp($item,"reference")==0) { ?>
                Below is a list of research groups and their phosphorylation data which have been deposited into P<sup>3</sup>DB:
                <table border="1">
                        <tr><td>Group</td><td>Data</td><td>Reference</td></tr>
                        <tr><td>Thelen lab</td><td>Phosphorylation on oilseed rape</td><td>To be published</td></tr>
                        <tr><td>Ishihama lab</td><td>Phosphorylation on <i>Arabidopsis thaliana</i></td><td>Sugiyama,N., Nakagami,H., Mochida,K., Daudi,A., 
                        Tomita,M., Shirasu,K. and Ishihama,Y. (2008) Large-scale phosphorylation mapping reveals the extent of tyrosine
                        phosphorylation in Arabidopsis. <i>Mol Syst Biol.</i>, 4, 193.</td></tr>
                </table>
<?php
        } else {
                echo "TBD";
        }
}
?>

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